Deciphering the C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

We have used FACS to isolate fluorescent cells at multiple time points from synchronized embryos containing early and highly specific tissue/lineage markers. We then carried out RNA-seq, and observe dramatic differences in gene expression levels both between cell-types, and over time within the same population. Furthermore, we observe differential transcript usage between cell-types and over time, including differential promoter and differential exon usage that leads to additional differences between cell types.